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parser
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feature: added support for custom configuration

This commit is contained in:
Steve Nyemba 2020-12-21 23:28:22 -06:00
parent fe6b2ee3e8
commit 2beddab6b4
6 changed files with 170 additions and 91 deletions
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31
README.md
View File

@ -22,14 +22,38 @@ We wrote this frame to be used in both command line or as a library within in yo
pip install --upgrade git+https://hiplab.mc.vanderbilt.edu/git/lab/parse-edi.git
## Usage
cli:
healthcare-io.py --<[signup|init]> <email> --store <sqlite|mongo> [--batch <value>]
healthcare-io.py --parse --folder <path> [--batch <value>] [--resume]
healthcare-io.py --check-update
action :
--signup|init signup user and get configuration file
--parse starts parsing
--check checks for updates
parameters :
--<[signup|init]> signup or get a configuration file from a parsing server
--folder location of the files (the program will recursively traverse it)
--store data store mongo or sqlite or mongodb
--resume will attempt to resume if there was an interruption
**cli :**
1. signup to get parsing configuration
The parser is driven by a configuration, file you need by signing up.
healthcare-io.py --signup <email> [--store <mongo|sqlite>]
2. parsing claims in a folder
2. check version
Occasionally the attributes in the configuration file may change, This function will determine if there is a new version available.
healthcare-io.py --check-update
3. parsing data in a folder
The parser will recursively traverse a directory with claims and or remittances
healthcare-io.py --parse <claims|remits> --folder <path> [--batch <n>] [--resume]
@ -39,11 +63,6 @@ We wrote this frame to be used in both command line or as a library within in yo
--batch number of processes to spawn to parse the files
--resume tells the parser to resume parsing
if all files weren't processed or new files were added into the folder
3. dashboard
There is a built-in dashboard that has displays descriptive analytics in a web browser
healthcare-io.py --server <port> [--context <name>]
**Embedded in Code :**

2
healthcareio/__init__.py
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@ -17,4 +17,6 @@ Usage :
from healthcareio import analytics
import healthcareio.x12 as x12
import healthcareio.params as params
# from healthcareio import server

119
healthcareio/healthcare-io.py
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@ -32,9 +32,10 @@ Usage :
from healthcareio.params import SYS_ARGS
from transport import factory
import requests
from healthcareio import analytics
from healthcareio import server
from healthcareio.parser import get_content
import os
import json
@ -56,10 +57,10 @@ if not os.path.exists(PATH) :
import platform
import sqlite3 as lite
# PATH = os.sep.join([os.environ['HOME'],'.edi-parser'])
def register (**args) :
def signup (**args) :
"""
:email user's email address
:url url of the provider to register
:url url of the provider to signup
"""
email = args['email']
@ -203,12 +204,27 @@ def upgrade(**args):
"""
url = args['url'] if 'url' in args else URL+"/upgrade"
headers = {"key":args['key'],"email":args["email"],"url":url}
def check(**_args):
"""
This function will check if there is an update available (versions are in the configuration file)
:param url
"""
url = _args['url'][:-1] if _args['url'].endswith('/') else _args['url']
url = url + "/version"
if 'version' not in _args :
version = {"_id":"version","current":0.0}
else:
version = _args['version']
http = requests.session()
r = http.get(url)
return r.json()
if __name__ == '__main__' :
info = init()
if 'out-folder' in SYS_ARGS :
OUTPUT_FOLDER = SYS_ARGS['out-folder']
SYS_ARGS['url'] = SYS_ARGS['url'] if 'url' in SYS_ARGS else URL
if set(list(SYS_ARGS.keys())) & set(['signup','init']):
#
@ -217,10 +233,10 @@ if __name__ == '__main__' :
#
email = SYS_ARGS['signup'].strip() if 'signup' in SYS_ARGS else SYS_ARGS['init']
url = SYS_ARGS['url'] if 'url' in SYS_ARGS else 'https://healthcareio.the-phi.com'
url = SYS_ARGS['url'] if 'url' in SYS_ARGS else URL
store = SYS_ARGS['store'] if 'store' in SYS_ARGS else 'sqlite'
db='healthcareio' if 'db' not in SYS_ARGS else SYS_ARGS['db']
register(email=email,url=url,store=store,db=db)
signup(email=email,url=url,store=store,db=db)
# else:
# m = """
# usage:
@ -244,11 +260,17 @@ if __name__ == '__main__' :
if 'file' in SYS_ARGS :
files = [SYS_ARGS['file']] if not os.path.isdir(SYS_ARGS['file']) else []
if 'folder' in SYS_ARGS and os.path.exists(SYS_ARGS['folder']):
names = os.listdir(SYS_ARGS['folder'])
files += [os.sep.join([SYS_ARGS['folder'],name]) for name in names if not os.path.isdir(os.sep.join([SYS_ARGS['folder'],name]))]
for root,_dir,f in os.walk(SYS_ARGS['folder']) :
if f :
files += [os.sep.join([root,name]) for name in f]
# names = os.listdir(SYS_ARGS['folder'])
# files += [os.sep.join([SYS_ARGS['folder'],name]) for name in names if not os.path.isdir(os.sep.join([SYS_ARGS['folder'],name]))]
else:
#
# raise an erro
# raise an error
pass
#
# if the user has specified to resume, we should look into the logs and pull the files processed and those that haven't
@ -256,40 +278,13 @@ if __name__ == '__main__' :
if 'resume' in SYS_ARGS :
store_config = json.loads( (open(os.sep.join([PATH,'config.json']))).read() )
files = proxy.get.resume(files,store_config )
print (["Found ",len(files)," files unprocessed"])
# print (["Found ",len(files)," files unprocessed"])
#
# @TODO: Log this here so we know what is being processed or not
SCOPE = None
if files : #and ('claims' in SYS_ARGS['parse'] or 'remits' in SYS_ARGS['parse']):
# logger = factory.instance(type='disk.DiskWriter',args={'path':os.sep.join([info['out-folder'],SYS_ARGS['parse']+'.log'])})
# if info['store']['type'] == 'disk.DiskWriter' :
# info['store']['args']['path'] += (os.sep + 'healthcare-io.json')
# elif info['store']['type'] == 'disk.SQLiteWriter' :
# # info['store']['args']['path'] += (os.sep + 'healthcare-io.db3')
# pass
# if info['store']['type'] == 'disk.SQLiteWriter' :
# info['store']['args']['table'] = SYS_ARGS['parse'].strip().lower()
# _info = json.loads(json.dumps(info['store']))
# _info['args']['table']='logs'
# else:
# #
# # if we are working with no-sql we will put the logs in it (performance )?
# info['store']['args']['doc'] = SYS_ARGS['parse'].strip().lower()
# _info = json.loads(json.dumps(info['store']))
# _info['args']['doc'] = 'logs'
# logger = factory.instance(**_info)
# writer = factory.instance(**info['store'])
#
# we need to have batches ready for this in order to run some of these queries in parallel
# @TODO: Make sure it is with a persistence storage (not disk .. not thread/process safe yet)
# - Make sure we can leverage this on n-cores later on, for now the assumption is a single core
#
BATCH_COUNT = 1 if 'batch' not in SYS_ARGS else int (SYS_ARGS['batch'])
files = np.array_split(files,BATCH_COUNT)
@ -308,26 +303,6 @@ if __name__ == '__main__' :
while len(procs) > 0 :
procs = [proc for proc in procs if proc.is_alive()]
time.sleep(2)
# for filename in files :
# if filename.strip() == '':
# continue
# # content,logs = get_content(filename,CONFIG,CONFIG['SECTION'])
# #
# try:
# content,logs = parse(filename = filename,type=SYS_ARGS['parse'])
# if content :
# writer.write(content)
# if logs :
# [logger.write(dict(_row,**{"parse":SYS_ARGS['parse']})) for _row in logs]
# else:
# logger.write({"parse":SYS_ARGS['parse'],"name":filename,"completed":True,"rows":len(content)})
# except Exception as e:
# logger.write({"parse":SYS_ARGS['parse'],"filename":filename,"completed":False,"rows":-1,"msg":e.args[0]})
# # print ([filename,len(content)])
# #
# # @TODO: forward this data to the writer and log engine
# #
@ -358,6 +333,28 @@ if __name__ == '__main__' :
pointer = lambda : server.app.run(host='0.0.0.0',port=PORT,debug=DEBUG,threaded=False)
pthread = Process(target=pointer,args=())
pthread.start()
elif 'check-update' in SYS_ARGS :
_args = {"url":SYS_ARGS['url']}
try:
if os.path.exists(os.sep.join([PATH,'config.json'])) :
SYS_ARGS['config'] = json.loads((open(os.sep.join([PATH,'config.json']))).read())
else:
SYS_ARGS['config'] = {}
if 'version' in SYS_ARGS['config'] :
_args['version'] = SYS_ARGS['config']['version']
version = check(**_args)
_version = {"current":0.0}if 'version' not in SYS_ARGS['config'] else SYS_ARGS['config']['version']
if _version['current'] != version['current'] :
print ()
print ("You need to upgrade your system to version to ",version['current'])
print ("\t- signup (for new configuration)")
print ("\t- use pip to upgrade the codebase")
else:
print ()
print ("You are running the current configuraiton version ",_version.current)
except Exception as e:
print (e)
pass
elif 'export' in SYS_ARGS:
#
@ -373,11 +370,15 @@ if __name__ == '__main__' :
cli:
healthcare-io.py --<[signup|init]> <email> --store <sqlite|mongo> [--batch <value>]
healthcare-io.py --parse claims --folder <path> [--batch <value>]
healthcare-io.py --parse remits --folder <path> [--batch <value>] [--resume]
healthcare-io.py --parse --folder <path> [--batch <value>] [--resume]
healthcare-io.py --check-update
action :
--signup|init signup user and get configuration file
--parse starts parsing
--check checks for updates
parameters :
--<[signup|init]> signup or get a configuration file from a parsing server
--folder location of the files (the program will recursively traverse it)
--store data store mongo or sqlite or mongodb
--resume will attempt to resume if there was an interruption
"""

20
healthcareio/server/__init__.py
View File

@ -11,11 +11,11 @@ import numpy as np
from healthcareio import x12
from multiprocessing import Process
from flask_socketio import SocketIO, emit, disconnect,send
# from flask_socketio import SocketIO, emit, disconnect,send
from healthcareio.server import proxy
PATH = os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
app = Flask(__name__)
socket_ = SocketIO(app)
# socket_ = SocketIO(app)
def resume (files):
_args = SYS_ARGS['config']['store'].copy()
@ -30,7 +30,7 @@ def resume (files):
_files = [item['name'] for item in _files]
except Exception as e :
pass
print (["found ",len(files),"\tProcessed ",len(_files)])
return list(set(files) - set(_files))
@ -66,14 +66,14 @@ def push() :
_args = {"aggregate":"logs","cursor":{},"allowDiskUse":True,"pipeline":pipeline}
r = pd.DataFrame(reader.read(mongo=_args))
r = healthcareio.analytics.Apex.apply({"chart":{"type":"donut","axis":{"x":"count","y":"type"}},"data":r})
emit("update",r,json=True)
# emit("update",r,json=True)
return r
@socket_.on('connect')
def client_connect(**r):
print ('Connection received')
print (r)
push()
pass
# @socket_.on('connect')
# def client_connect(**r):
# print ('Connection received')
# print (r)
# push()
# pass
@app.route("/favicon.ico")
def _icon():

2
healthcareio/server/proxy.py
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@ -32,7 +32,7 @@ class get :
_files = [item['name'] for item in _files]
except Exception as e :
pass
print (["found ",len(files),"\tProcessed ",len(_files)])
print ( [len(list(set(files) - set(_files))),' files to be processed'])
return list(set(files) - set(_files))
@staticmethod

79
healthcareio/x12/__init__.py
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@ -24,6 +24,7 @@ import sys
from itertools import islice
from multiprocessing import Process
import transport
import jsonmerge
class void :
pass
class Formatters :
@ -95,7 +96,6 @@ class Formatters :
if _row[0] in config['SIMILAR'] :
key = config['SIMILAR'][_row[0]]
_info = config[key]
return _info
def hash(self,value):
@ -181,13 +181,16 @@ class Formatters :
return x
class Parser (Process):
def __init__(self,path):
"""
:path path of the configuration file (it can be absolute)
"""
Process.__init__(self)
self.utils = Formatters()
self.get = void()
self.get.value = self.get_map
self.get.default_value = self.get_default_value
_config = json.loads(open(path).read())
self._custom_config = self.get_custom(path)
self.config = _config['parser']
self.store = _config['store']
@ -197,6 +200,27 @@ class Parser (Process):
self.emit = void()
self.emit.pre = None
self.emit.post = None
def get_custom(self,path) :
"""
:path path of the configuration file (it can be absolute)
"""
#
#
_path = path.replace('config.json','')
if _path.endswith(os.sep) :
_path = _path[:-1]
_config = {}
_path = os.sep.join([_path,'custom'])
if os.path.exists(_path) :
files = os.listdir(_path)
if files :
fullname = os.sep.join([_path,files[0]])
_config = json.loads ( (open(fullname)).read() )
return _config
def set_files(self,files):
self.files = files
def get_map(self,row,config,version=None):
@ -247,15 +271,18 @@ class Parser (Process):
value = {key:value} if key not in value else value
else:
if 'syn' in config and value in config['syn'] :
value = config['syn'][value]
if type(value) == dict :
object_value = dict(object_value, **value)
else:
object_value[key] = value
else:
#
# we are dealing with a complex object
@ -275,26 +302,35 @@ class Parser (Process):
return object_value
def apply(self,content,_code) :
"""
:file content i.e a segment with the envelope
:content content of a file i.e a segment with the envelope
:_code 837 or 835 (helps get the appropriate configuration)
"""
util = Formatters()
# header = default_value.copy()
value = {}
for row in content[:] :
row = util.split(row.replace('\n','').replace('~',''))
_info = util.get.config(self.config[_code][0],row)
if self._custom_config and _code in self._custom_config:
_cinfo = util.get.config(self._custom_config[_code],row)
else:
_cinfo = {}
# _info = self.consolidate(row=row,type=_code,config=_info,util=util)
# print ([row[0],_info])
# print ()
# continue
# _cinfo = util.get.config(self._custom_config[_code],row)
if _info :
try:
try:
_info = jsonmerge.merge(_info,_cinfo)
tmp = self.get.value(row,_info)
# if 'P1080351470' in content[0] and 'PLB' in row:
# print (_info)
# print (row)
# print (tmp)
if not tmp :
continue
if 'label' in _info :
@ -326,7 +362,9 @@ class Parser (Process):
elif 'field' in _info :
name = _info['field']
value[name] = tmp
# value[name] = tmp
value = jsonmerge.merge(value,{name:tmp})
else:
@ -341,6 +379,7 @@ class Parser (Process):
return value if value else {}
def get_default_value(self,content,_code):
util = Formatters()
TOP_ROW = content[1].split('*')
CATEGORY= content[2].split('*')[1].strip()
@ -359,6 +398,8 @@ class Parser (Process):
value['payer_id'] = SENDER_ID
else:
value['provider_id'] = SENDER_ID
#
# Let's parse this for default values
return value
def read(self,filename) :
@ -381,8 +422,14 @@ class Parser (Process):
INITIAL_ROWS = file[:4]
if len(INITIAL_ROWS) < 3 :
return None,[{"name":filename,"completed":False}],None
section = 'HL' if INITIAL_ROWS[1].split('*')[1] == 'HC' else 'CLP'
_code = '837' if section == 'HL' else '835'
# section = 'HL' if INITIAL_ROWS[1].split('*')[1] == 'HC' else 'CLP'
# _code = '837' if section == 'HL' else '835'
# print ([_code,section])
_code = INITIAL_ROWS[2].split('*')[1].strip()
# section = 'CLP' if _code == '835' else 'HL'
section = self.config[_code][0]['SECTION'].strip()
#
# adjusting the
DEFAULT_VALUE = self.get.default_value(INITIAL_ROWS,_code)
DEFAULT_VALUE['name'] = filename.strip()
#
@ -390,22 +437,30 @@ class Parser (Process):
# index 1 identifies file type i.e CLM for claim and CLP for remittance
segment = []
index = 0;
_toprows = []
for row in file :
row = row.replace('\r','')
if not segment and not row.startswith(section):
_toprows += [row]
if row.startswith(section) and not segment:
segment = [row]
continue
elif segment and not row.startswith(section):
segment.append(row)
if len(segment) > 1 and row.startswith(section):
#
# process the segment somewhere (create a thread maybe?)
#
# default_claim = dict({"index":index},**DEFAULT_VALUE)
# print (_toprows)
_claim = self.apply(segment,_code)
# if _claim['claim_id'] == 'P1080351470' :
# print (_claim)
# _claim = dict(DEFAULT_VALUE,**_claim)
@ -425,12 +480,14 @@ class Parser (Process):
claim = self.apply(segment,_code)
if claim :
claim['index'] = len(claims)
claim = jsonmerge.merge(claim,self.apply(_toprows,_code))
claims.append(dict(DEFAULT_VALUE,**claim))
if type(file) != list :
file.close()
# x12_file = open(filename.strip(),errors='ignore').read().split('\n')
except Exception as e:
logs.append ({"parse":_code,"completed":False,"name":filename,"msg":e.args[0]})
return [],logs,None